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netcdf-c/ncdump/CMakeLists.txt
Dennis Heimbigner 751300ec59 Fix more memory leaks in netcdf-c library 
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173

Sorry that it is so big, but leak suppression can be complex.

This PR fixes all remaining memory leaks -- as determined by
-fsanitize=address, and with the exceptions noted below.

Unfortunately. there remains a significant leak that I cannot
solve. It involves vlens, and it is unclear if the leak is
occurring in the netcdf-c library or the HDF5 library.

I have added a check_PROGRAM to the ncdump directory to show the
problem.  The program is called tst_vlen_demo.c To exercise it,
build the netcdf library with -fsanitize=address enabled. Then
go into ncdump and do a "make clean check".  This should build
tst_vlen_demo without actually executing it.  Then do the
command "./tst_vlen_demo" to see the output of the memory
checker.  Note the the lost malloc is deep in the HDF5 library
(in H5Tvlen.c).

I am temporarily working around this error in the following way.
1. I modified several test scripts to not execute known vlen tests
   that fail as described above.
2. Added an environment variable called NC_VLEN_NOTEST.
   If set, then those specific tests are suppressed.

This should mean that the --disable-utilities option to
./configure should not need to be set to get a memory leak clean
build.  This should allow for detection of any new leaks.

Note: I used an environment variable rather than a ./configure
option to control the vlen tests. This is because it is
temporary (I hope) and because it is a bit tricky for shell
scripts to access ./configure options.

Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-15 10:00:38 -07:00

288 lines
9.4 KiB
CMake
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IF(BUILD_SHARED_LIBS AND WIN32)
remove_definitions(-DDLL_EXPORT)
remove_definitions(-DDLL_NETCDF)
ENDIF()
SET(ncdump_FILES ncdump.c vardata.c dumplib.c indent.c nctime0.c utils.c nciter.c)
SET(nccopy_FILES nccopy.c nciter.c chunkspec.c utils.c dimmap.c list.c)
SET(ocprint_FILES ocprint.c)
IF(USE_X_GETOPT)
SET(ncdump_FILES ${ncdump_FILES} XGetopt.c)
SET(nccopy_FILES ${nccopy_FILES} XGetopt.c)
SET(ocprint_FILES ${ocprint_FILES} XGetopt.c)
ENDIF()
ADD_EXECUTABLE(ncdump ${ncdump_FILES})
ADD_EXECUTABLE(nccopy ${nccopy_FILES})
IF(ENABLE_DAP)
ADD_EXECUTABLE(ocprint ${ocprint_FILES})
ENDIF(ENABLE_DAP)
TARGET_LINK_LIBRARIES(ncdump netcdf ${ALL_TLL_LIBS})
TARGET_LINK_LIBRARIES(nccopy netcdf ${ALL_TLL_LIBS})
IF(ENABLE_DAP)
TARGET_LINK_LIBRARIES(ocprint netcdf ${ALL_TLL_LIBS})
ENDIF(ENABLE_DAP)
####
# We have to do a little tweaking
# to remove the Release/ and Debug/ directories
# in MSVC builds. This is required to get
# test scripts to work.
####
IF(MSVC)
SET_TARGET_PROPERTIES(ncdump PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncdump PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncdump PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nccopy PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nccopy PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nccopy PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
IF(ENABLE_DAP)
SET_TARGET_PROPERTIES(ocprint PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ocprint PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ocprint PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
ENDIF(ENABLE_DAP)
ENDIF()
IF(ENABLE_TESTS)
ADD_EXECUTABLE(rewrite-scalar rewrite-scalar.c)
ADD_EXECUTABLE(bom bom.c)
ADD_EXECUTABLE(tst_dimsizes tst_dimsizes.c)
ADD_EXECUTABLE(nctrunc nctrunc.c)
TARGET_LINK_LIBRARIES(rewrite-scalar netcdf)
TARGET_LINK_LIBRARIES(bom netcdf)
TARGET_LINK_LIBRARIES(tst_dimsizes netcdf)
IF(USE_NETCDF4)
ADD_EXECUTABLE(tst_fileinfo tst_fileinfo.c)
TARGET_LINK_LIBRARIES(tst_fileinfo netcdf)
ENDIF()
IF(MSVC)
SET_TARGET_PROPERTIES(rewrite-scalar PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(rewrite-scalar PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(rewrite-scalar PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(bom PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(bom PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(bom PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_dimsizes PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_dimsizes PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_dimsizes PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
IF(USE_NETCDF4)
SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
ENDIF(USE_NETCDF4)
ENDIF(MSVC)
# Base tests
# The tests are set up as a combination of shell scripts and executables that
# must be run in a particular order. It is painful but will use macros to help
# keep it from being too bad.
## Start adding tests in the appropriate order
add_sh_test(ncdump run_tests)
add_sh_test(ncdump tst_64bit)
add_bin_test_no_prefix(ref_ctest)
add_bin_test_no_prefix(ref_ctest64)
add_sh_test(ncdump tst_output)
add_sh_test(ncdump tst_lengths)
add_sh_test(ncdump tst_calendars)
build_bin_test_no_prefix(tst_utf8)
add_sh_test(ncdump run_utf8_tests)
IF(USE_NETCDF4)
add_sh_test(ncdump run_utf8_nc4_tests)
add_sh_test(ncdump tst_fileinfo)
add_sh_test(ncdump tst_hdf5_offset)
ENDIF(USE_NETCDF4)
add_sh_test(ncdump tst_null_byte_padding)
IF(USE_STRICT_NULL_BYTE_HEADER_PADDING)
SET_TESTS_PROPERTIES(ncdump_tst_null_byte_padding PROPERTIES WILL_FAIL TRUE)
ENDIF(USE_STRICT_NULL_BYTE_HEADER_PADDING)
add_sh_test(ncdump tst_nccopy3)
IF(HAVE_BASH)
SET_TESTS_PROPERTIES(ncdump_tst_nccopy3 PROPERTIES RUN_SERIAL TRUE)
ENDIF(HAVE_BASH)
add_sh_test(ncdump tst_nccopy3_subset)
add_sh_test(ncdump tst_charfill)
add_sh_test(ncdump tst_formatx3)
add_sh_test(ncdump tst_bom)
add_sh_test(ncdump tst_dimsizes)
# The following test script invokes
# gcc directly.
IF(CMAKE_COMPILER_IS_GNUCC OR APPLE)
IF(ENABLE_LARGE_FILE_TESTS)
add_sh_test(ncdump tst_iter)
ENDIF(ENABLE_LARGE_FILE_TESTS)
ENDIF(CMAKE_COMPILER_IS_GNUCC OR APPLE)
add_sh_test(ncdump tst_inmemory_nc3)
IF(USE_NETCDF4)
add_sh_test(ncdump tst_inmemory_nc4)
ENDIF(USE_NETCDF4)
IF(USE_NETCDF4)
build_bin_test_no_prefix(tst_create_files)
build_bin_test_no_prefix(tst_group_data)
build_bin_test_no_prefix(tst_enum_data)
build_bin_test_no_prefix(tst_opaque_data)
build_bin_test_no_prefix(tst_string_data)
build_bin_test_no_prefix(tst_vlen_data)
build_bin_test_no_prefix(tst_comp)
build_bin_test_no_prefix(tst_comp2)
build_bin_test_no_prefix(tst_nans)
build_bin_test_no_prefix(tst_h_scalar)
add_sh_test(ncdump tst_formatx4)
# Add this test by hand, as it is also called from a script.
# Editing the script would break autotools compatibility.
build_bin_test_no_prefix(tst_special_atts)
build_bin_test_no_prefix(tst_compress)
build_bin_test_no_prefix(tst_chunking)
###
# This test fails on Visual Studio builds with bash.
# It passes, but technically fails because the scientific
# formatting omits a 0.
###
IF(EXTRA_TESTS)
add_sh_test(ncdump run_back_comp_tests)
IF(MSVC)
SET_TESTS_PROPERTIES(ncdump_run_back_comp_tests PROPERTIES WILL_FAIL TRUE)
ENDIF(MSVC)
ENDIF(EXTRA_TESTS)
# Known failure on MSVC; the number of 0's padding
# is different, but the result is actually correct.
IF(HAVE_BASH)
add_sh_test(ncdump tst_netcdf4)
build_bin_test_no_prefix(tst_h_rdc0)
ENDIF()
build_bin_test_no_prefix(tst_unicode)
build_bin_test_no_prefix(tst_fillbug)
add_sh_test(ncdump_sh tst_fillbug)
add_sh_test(ncdump tst_netcdf4_4)
IF(MSVC AND HAVE_BASH)
SET_TESTS_PROPERTIES(ncdump_tst_netcdf4_4 PROPERTIES WILL_FAIL TRUE)
ENDIF(MSVC AND HAVE_BASH)
###
# Some test reordering was required to ensure these tests
# only ran after ncdump was built.
###
add_sh_test(ncdump run_ncgen_tests)
IF(USE_NETCDF4)
add_sh_test(ncdump run_ncgen_nc4_tests)
ENDIF(USE_NETCDF4)
add_sh_test(ncdump tst_grp_spec)
add_sh_test(ncdump tst_mud)
add_sh_test(ncdump_shell tst_h_scalar)
add_sh_test(ncdump tst_nccopy4)
IF(HAVE_BASH)
SET_TESTS_PROPERTIES(ncdump_tst_nccopy4 PROPERTIES RUN_SERIAL TRUE)
ENDIF(HAVE_BASH)
add_sh_test(ncdump tst_nccopy5)
IF(HAVE_BASH)
SET_TESTS_PROPERTIES(ncdump_tst_nccopy5 PROPERTIES RUN_SERIAL TRUE)
ENDIF(HAVE_BASH)
IF(USE_NETCDF4)
add_sh_test(ncdump tst_ncgen4)
ENDIF(USE_NETCDF4)
add_sh_test(ncdump tst_inttags)
IF(USE_NETCDF4)
add_sh_test(ncdump tst_inttags4)
ENDIF(USE_NETCDF4)
ENDIF()
ENDIF()
IF(MSVC)
SET_TARGET_PROPERTIES(ncdump
PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
)
SET_TARGET_PROPERTIES(nccopy
PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
)
IF(ENABLE_DAP)
SET_TARGET_PROPERTIES(ocprint
PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
)
ENDIF(ENABLE_DAP)
ENDIF()
INSTALL(TARGETS ncdump RUNTIME DESTINATION bin COMPONENT utilities)
INSTALL(TARGETS nccopy RUNTIME DESTINATION bin COMPONENT utilities)
SET(MAN_FILES nccopy.1 ncdump.1)
# Note, the L512.bin file is file containing exactly 512 bytes each of value 0.
# It is used for creating hdf5 files with varying offsets for testing.
FILE(GLOB COPY_FILES ${CMAKE_BINARY_DIR}/ncgen/*.nc ${CMAKE_BINARY_DIR}/nc_test4/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/*.ncml ${CMAKE_CURRENT_SOURCE_DIR}/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/*.cdl ${CMAKE_CURRENT_SOURCE_DIR}/*.sh ${CMAKE_CURRENT_SOURCE_DIR}/*.1 ${CMAKE_CURRENT_SOURCE_DIR}/L512.bin)
FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE)
ADD_SUBDIRECTORY(cdl)
ADD_SUBDIRECTORY(expected)
SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${CLEANFILES}")
IF(NOT MSVC)
INSTALL(FILES ${MAN_FILES} DESTINATION "share/man/man1" COMPONENT documentation)
ENDIF()
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